Fix: Don't drop disabled cells

src/analysis/Topology.jl

@@ -58,12 +58,18 @@ function set_unresolved(topology::NotebookTopology, unresolved_cells::Vector{Cel
 end
 
 
-function Base.setdiff(topology::NotebookTopology, cells::Vector{Cell})
+"""
+    exclude_roots(topology::NotebookTopology, roots_to_exclude)::NotebookTopology
+
+Returns a new topology as if `topology` was created with all code for `roots_to_exclude`
+being empty, preserving disabled cells and cell order.
+"""
+function exclude_roots(topology::NotebookTopology, cells::Vector{Cell})
     NotebookTopology(
         nodes=setdiffkeys(topology.nodes, cells),
         codes=setdiffkeys(topology.codes, cells),
         unresolved_cells=ImmutableSet{Cell}(setdiff(topology.unresolved_cells.c, cells); skip_copy=true),
-        cell_order=ImmutableVector{Cell}(setdiff(topology.cell_order.c, cells); skip_copy=true),
-        disabled_cells=ImmutableSet{Cell}(setdiff(topology.disabled_cells.c, cells); skip_copy=true),
+        cell_order=topology.cell_order,
+        disabled_cells=topology.disabled_cells,
     )
 end

src/evaluation/Run.jl

@@ -100,8 +100,8 @@ function run_reactive_core!(
         cell.queued = false
         cell.depends_on_disabled_cells = true
     end
-	
-	new_topology = setdiff(new_topology, indirectly_deactivated)
+
+	new_topology = exclude_roots(new_topology, indirectly_deactivated)
 
     # save the old topological order - we'll delete variables assigned from its
     # and re-evalutate its cells unless the cells have already run previously in the reactive run

src/notebook/saving and loading.jl

@@ -56,18 +56,24 @@ function save_notebook(io::IO, notebook::Notebook)
     println(io)
 
     cells_ordered = collect(topological_order(notebook))
-
+    # TODO: add test for this case
+    if length(cells_ordered) != length(notebook.cells)
+        cells = notebook.cells
+        updated_topo = updated_topology(notebook.topology, notebook, cells)
+        cells_ordered = collect(topological_order(updated_topo, cells))
+    end
+
     for c in cells_ordered
         println(io, _cell_id_delimiter, string(c.cell_id))
-        
+
         let metadata_toml = strip(sprint(TOML.print, get_metadata_no_default(c)))
             if metadata_toml != ""
                 for line in split(metadata_toml, "\n")
                     println(io, _cell_metadata_prefix, line)
                 end
             end
         end
-        
+
         if must_be_commented_in_file(c)
             print(io, _disabled_prefix)
             print(io, replace(c.code, _cell_id_delimiter => "# "))

test/cell_disabling.jl

@@ -345,3 +345,46 @@ end
 
     WorkspaceManager.unmake_workspace((🍭, notebook))
 end
+
+@testset "Disabled cells should stay in the topology (#2676)" begin
+    🍭 = ServerSession()
+    notebook = Notebook(Cell.([
+        "using Dates",
+        "b = 2; December",
+        "b",
+    ]))
+
+    disabled_cell = notebook.cells[end]
+    Pluto.set_disabled(disabled_cell, true)
+    @test is_disabled(disabled_cell)
+
+    old_topo = notebook.topology
+    @test count(Pluto.is_disabled, notebook.cells) == 1
+    order = update_run!(🍭, notebook, notebook.cells)
+
+    # Disabled
+    @test length(order.input_topology.disabled_cells) == 1
+    @test disabled_cell ∈ order.input_topology.disabled_cells
+    runned_cells = collect(order)
+    @test length(runned_cells) == 2
+    @test disabled_cell ∉ runned_cells
+
+    topo = notebook.topology
+    @test old_topo !== topo # topology was updated
+
+    order = Pluto.topological_order(notebook)
+
+    @test length(order.input_topology.disabled_cells) == 1
+    @test disabled_cell ∈ order.input_topology.disabled_cells
+    saved_cells = collect(order)
+    @test length(saved_cells) == length(notebook.cells)
+    @test issetequal(saved_cells, notebook.cells)
+
+    io = IOBuffer()
+    Pluto.save_notebook(io, notebook)
+    seekstart(io)
+    notebook2 = Pluto.load_notebook_nobackup(io, "mynotebook.jl")
+    @test length(notebook2.cells) == length(notebook.cells)
+
+    WorkspaceManager.unmake_workspace((🍭, notebook))
+end